Firstly, I bought a new cheaper USBASP programmer, and made nice little PCBs to burn each microcontroller. This is the ATTINY2313 circuit.
By publiccpervert at 2012-07-03
By publiccpervert at 2012-07-03

Reduced a official N64 controller board
By publiccpervert at 2012-07-03

Opened space for the N64 controller board
By publiccpervert at 2012-07-03

Lastly, the controller itself before close. On the first part, you can see the MiniUSB port for charging the battery, charging circuit, and the wirelles module.
On the second part you can see batteries, 3,3v regulator (under the left black tape), joysticks, ATTINY2313 to mimic the N64 signals to the wirelles module, and I used an ATMEGA8 again (under this black tape on the middle) to make the conversion POT JOYSTICK > PHOTO DIODE JOYSTICK
By publiccpervert at 2012-07-03

Sure it beats those crappy IR pads! A good thing is that the controller uses a kind of universal protocol and can be compatible with some consoles.
Actually the creator of this project isn't me (I've built this unit, of course), but from an awesome guy called Micro, from gamesx.com. He did all the hard work. Take a look on a video he made: